Variant report

Variant	rs12022603
Chromosome Location	chr1:85396800-85396801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85396013-85396900	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:85396026-85396960	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:85396542-85396921	GM12891	blood:	n/a	n/a
4	STAT3	chr1:85396664-85396851	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:85396432-85396897	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:85396016-85396896	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:85395951-85396950	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:85395974-85396959	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:85395884-85396907	GM12892	blood:	n/a	n/a
10	STAT3	chr1:85396566-85396836	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:85396244-85396929	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
MCOLN2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12032056	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12406236	1.00[JPT][hapmap]
rs678065	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85385600-85403200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:85386200-85398400	Weak transcription	Fetal Intestine Large	intestine
3	chr1:85389400-85405600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:85390800-85401800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:85391800-85405800	Weak transcription	Small Intestine	intestine
6	chr1:85392200-85397000	Strong transcription	GM12878-XiMat	blood
7	chr1:85395400-85396800	Enhancers	Primary T cells from cord blood	blood
8	chr1:85395400-85396800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:85395400-85405800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:85395600-85396800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:85395600-85396800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:85395600-85397000	Enhancers	Fetal Thymus	thymus
13	chr1:85395800-85397000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:85396000-85396800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:85396400-85410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:85396600-85401600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:85396600-85410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:85396800-85401600	Weak transcription	Primary T cells from cord blood	blood
19	chr1:85396800-85401600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:85396800-85401800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:85396800-85401800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:85396800-85404600	Weak transcription	Primary T cells fromperipheralblood	blood

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